Contacts of the helix formed by residues 20 - 35 (chain H) in PDB entry 1O1F
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 20 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A MLY 5.5 14.6 - - + +
19H PHE* 1.3 74.6 - - - +
21H GLU* 1.3 62.9 - - - +
22H THR* 3.1 12.5 + - - -
23H GLU* 3.0 61.4 + - - +
24H ILE* 3.2 12.3 + - - +
93H PRO* 4.4 18.5 - - + +
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Residues in contact with GLU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837A MLY 6.2 3.8 - - + -
838A ILE* 4.0 30.7 - - - +
841A LEU* 4.2 12.5 - - - +
53B ALA 4.9 2.3 - - - +
54B MET* 3.9 25.8 - - - +
19H PHE 4.0 0.8 + - - -
20H ASP* 1.3 74.0 - - - +
22H THR* 1.3 56.9 + - - +
24H ILE* 3.2 15.2 + - + +
25H GLU* 2.9 49.5 + - + +
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Residues in contact with THR 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841A LEU* 5.2 9.2 - - - +
20H ASP* 3.1 9.2 + - - -
21H GLU* 1.3 77.7 - - - +
23H GLU* 1.3 57.4 + - - +
25H GLU* 3.1 17.8 + - + +
26H ASP* 2.9 45.8 + - - +
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Residues in contact with GLU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839G MLY 5.3 9.0 - - - -
19H PHE* 3.3 26.7 - - + -
20H ASP* 3.0 46.1 + - - +
22H THR* 1.3 77.6 - - - +
24H ILE* 1.3 55.7 + - - +
26H ASP* 3.2 14.2 + - - +
27H PHE* 3.1 52.2 + - + -
88H LEU* 5.8 1.4 - - - +
91H ALA* 5.0 12.6 - - - +
93H PRO* 5.8 4.8 - - - +
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Residues in contact with ILE 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY* 6.1 5.4 - - - -
19H PHE* 3.9 36.3 - - + +
20H ASP 3.2 15.0 + - - +
21H GLU* 3.2 16.8 + - + +
23H GLU* 1.3 77.7 - - - +
25H GLU* 1.3 56.8 + - + +
27H PHE* 3.2 9.9 + - - +
28H LYS* 2.9 26.4 + - - +
77H PHE* 3.9 18.8 - - + -
81H LEU* 4.4 16.4 - - + -
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Residues in contact with GLU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A LEU* 4.3 17.7 - - - +
21H GLU* 2.9 48.2 + - + +
22H THR* 3.1 20.1 + - + +
24H ILE* 1.3 76.1 - - + +
26H ASP* 1.3 59.2 + - - +
28H LYS* 3.2 23.7 + - - +
29H GLU* 3.0 41.2 + - - +
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Residues in contact with ASP 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835G PHE* 4.0 16.0 - - + -
839G MLY 4.2 22.9 - - - -
842G LEU* 4.2 7.7 - - + +
843G LYS 6.0 1.2 - - - -
22H THR* 2.9 41.3 + - - +
23H GLU* 3.2 12.4 + - - +
25H GLU* 1.3 76.8 - - - +
27H PHE* 1.3 58.7 + - - +
29H GLU* 3.2 18.7 + - - +
30H ALA* 3.0 28.2 + - - +
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Residues in contact with PHE 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832G MET* 5.0 1.6 - - + -
835G PHE* 3.1 45.3 - + - -
839G MLY 5.7 2.2 - - - -
19H PHE* 3.5 32.8 - + - -
23H GLU* 3.1 36.8 + - + -
24H ILE* 3.2 7.6 + - - +
26H ASP* 1.3 76.3 - - - +
28H LYS* 1.3 56.5 + - - +
30H ALA* 3.8 4.5 - - + +
31H PHE* 2.9 29.6 + - - +
77H PHE* 4.1 3.7 - - - -
80H PHE* 4.6 11.0 - + + -
81H LEU* 4.0 23.6 - - + -
84H PHE* 4.3 33.2 - + + -
88H LEU* 4.5 11.0 - - + -
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Residues in contact with LYS 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H ILE 2.9 13.1 + - - +
25H GLU* 3.2 25.9 + - - +
27H PHE* 1.3 76.0 - - - +
29H GLU* 1.3 80.0 + - - +
31H PHE* 3.3 7.2 + - + +
32H THR* 2.9 36.0 + - - +
77H PHE* 3.5 30.0 - - + -
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Residues in contact with GLU 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842G LEU* 3.9 26.7 - - + +
843G LYS 3.0 27.0 - - - +
25H GLU* 3.0 22.6 + - - +
26H ASP* 3.2 24.8 + - - +
28H LYS* 1.3 90.3 + - - +
30H ALA* 1.3 59.5 + - - +
32H THR* 3.2 8.3 + - - -
33H VAL* 3.0 34.1 + - + +
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Residues in contact with ALA 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835G PHE* 3.5 39.5 - - + -
838G ILE* 4.9 10.5 - - + -
842G LEU* 4.6 5.1 - - + +
26H ASP 3.0 7.9 + - - +
27H PHE* 3.8 5.8 - - + +
28H LYS 3.4 0.2 - - - -
29H GLU* 1.3 75.4 - - - +
31H PHE* 1.3 63.6 + - - +
33H VAL* 3.2 7.1 + - - +
34H ILE* 3.1 37.5 + - + +
80H PHE* 4.9 5.6 - - + -
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Residues in contact with PHE 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H PHE 2.9 19.1 + - - +
28H LYS* 3.4 11.7 - - + +
29H GLU 3.3 0.2 - - - -
30H ALA* 1.3 77.4 - - - +
32H THR* 1.3 61.8 + - - +
34H ILE 3.4 1.0 + - - -
35H ASP* 2.9 36.5 + - + +
40H GLY* 3.1 42.6 - - - -
41H ILE 4.2 0.9 - - - -
42H ILE* 3.5 27.7 - - + +
75H ILE* 3.4 19.7 - - + -
76H ASN 3.5 10.5 - - - -
77H PHE* 3.6 28.3 - + + -
80H PHE* 3.7 23.1 - + + -
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Residues in contact with THR 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H LYS* 2.9 21.8 + - - +
29H GLU* 3.2 8.2 + - - -
31H PHE* 1.3 83.1 - - - +
33H VAL* 1.3 63.5 + - + +
35H ASP* 3.3 23.7 - - - +
36H GLN* 4.6 2.1 - - - +
38H ALA* 6.2 4.9 - - + -
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Residues in contact with VAL 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838G ILE* 4.0 31.6 - - + -
841G LEU* 6.3 1.6 - - + -
842G LEU* 4.5 17.3 - - + -
29H GLU* 3.0 19.9 + - + +
30H ALA* 3.2 7.2 + - - +
32H THR* 1.3 80.5 - - + +
34H ILE* 1.3 60.6 + - + +
36H GLN* 3.5 13.9 + - - +
50H THR* 3.4 11.2 + - + +
54H MET* 4.4 6.7 - - + -
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Residues in contact with ILE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831G TRP* 3.9 16.8 - - + +
834G LEU* 3.7 29.8 - - + -
835G PHE* 6.3 0.9 - - - -
838G ILE* 5.7 2.0 - - + -
30H ALA* 3.1 23.8 + - + +
33H VAL* 1.3 81.5 - - + +
35H ASP* 1.3 60.2 + - - +
36H GLN* 3.2 3.0 + - - +
42H ILE* 3.8 16.4 - - + -
46H ASP* 3.0 25.9 - - - +
47H LEU* 3.8 28.5 - - + -
50H THR* 3.2 24.6 + - + +
51H PHE* 6.5 0.2 - - + -
80H PHE* 4.4 15.9 - - + -
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Residues in contact with ASP 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H PHE* 2.9 25.5 + - + +
32H THR* 3.3 15.4 - - - +
33H VAL 3.5 0.2 - - - -
34H ILE* 1.3 74.5 - - - +
36H GLN* 1.3 56.4 + - - +
37H ASN* 2.9 26.0 - - - +
38H ALA* 3.0 21.9 + - - +
39H ASP 3.3 3.1 + - - -
40H GLY* 3.0 26.3 + - - -
41H ILE 3.1 25.5 + - - +
42H ILE* 3.5 9.7 - - + -
46H ASP* 3.2 10.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il